New releases

Publication 18

Crowd surfing on micro-robotic cilia

19. Amphibious transport of fluids and solids by soft magnetic carpets

Demirörs AF, Aykut S, Ganzeboom S, et al.

Advanced Science, 202102510 (2021) [10.1002/advs.202102510] [download PDF]

Abstract

One of the major challenges in modern robotics is controlling micromanipulation by active and adaptive materials. In the respiratory system, such actuation enables pathogen clearance by means of motile cilia. While various types of artificial cilia have been engineered recently, they often involve complex manufacturing protocols and focus on transporting liquids only. Here, we create soft magnetic carpets via an easy self-assembly route based on the Rosensweig instability. These carpets can transport liquids but also solid objects that are larger and heavier than the artificial cilia, using a crowd-surfing effect. This amphibious transportation is locally and reconfigurably tuneable by simple micromagnets or advanced programmable magnetic fields with a high degree of spatial resolution. We identify and model two surprising cargo reversal effects due to collective ciliary motion and non-trivial elastohydrodynamics. While our active carpets are generally applicable to integrated control systems for transport, mixing and sorting, these effects could also be exploited for microfluidic viscosimetry and elastometry.

Publication 17

Cargo particles entrained by a swimming droplet

18. Collective entrainment and confinement amplify transport by schooling microswimmers

Jin C, Chen Y, Maass CC, Mathijssen AJTM

Physical Review Letters 127: 088006 (2021) [10.1103/PhysRevLett.127.088006] [download PDF]

Media coverage (selection):

  • Physics Magazine, by Philip Ball, “Microswimmers May Shepherd Large Liquid Volumes” (20 Aug 2021)
  • Penn Today, by Erica K. Brockmeier, “How schools of ‘microswimmers’ can increase their cargo capacity” (20 Aug 2021)
Abstract
Microswimmers can serve as cargo carriers that move deep inside complex flow networks. When a school collectively entrains the surrounding fluid, their transport capacity can be enhanced. This effect is quantified with good agreement between experiments with self-propelled droplets and a confined Brinkman squirmer model. The volume of liquid entrained can be much larger than the droplet itself, amplifying the effective cargo capacity over an order of magnitude, even for dilute schools. Hence, biological and engineered swimmers can efficiently transport materials into confined environments.
Publication 17

Biological actuators driving non-equilibrium diffusion from a surface

17. Active carpets drive non-equilibrium diffusion and enhanced molecular fluxes

Guzman-Lastra F, Löwen H, Mathijssen AJTM

Nature Communications 12: 1906 (2021) [10.1038/s41467-021-22029-y] [download PDF]

Media coverage (selection):

  • Penn Today, by Erica K. Brockmeier, “How cells transport molecules with ‘active carpets’” (6 March 2021)
  • Genetic Engineering & Biotechnology News, by Anjali A. Sarkar, PhD, “Scientists extend Fick’s laws of diffusion to explain movement over natural active carpets” (31 March 2021)
  • Pro-Physik, “Diffusion mit Mikrofluktuation”, in German (30 March 2021)
  • La Tercera, National newspaper in Chile, “Física chilena lidera estudio publicado en Nature que crea modelo matemático que predice por primera vez cómo se transportan las moléculas en organismos vivos”, in Spanish , published online & in print (3 April 2021)
Abstract
Biological activity is often highly concentrated on surfaces, across the scales from molecular motors and ciliary arrays to sessile and motile organisms. These ‘active carpets’ locally inject energy into their surrounding fluid. Whereas Fick’s laws of diffusion are established near equilibrium, it is unclear how to solve non-equilibrium transport driven by such boundary-actuated fluctuations. Here, we derive the enhanced diffusivity of molecules or passive particles as a function of distance from an active carpet. Following Schnitzer’s telegraph model, we then cast these results into generalised Fick’s laws. Two archetypal problems are solved using these laws: First, considering sedimentation towards an active carpet, we find a self-cleaning effect where surface-driven fluctuations can repel particles. Second, considering diffusion from a source to an active sink, say nutrient capture by suspension feeders, we find a large molecular flux compared to thermal diffusion. Hence, our results could elucidate certain non-equilibrium properties of active coating materials and life at interfaces.
Publication 18

Light-controlled molecular motors
(Image: Bryant Lab)

Engineering reconfigurable flow patterns via surface-driven light-controlled active matter

Gong X, Mathijssen AJTM, Bryant Z, Prakash M

Physical Review Fluids accepted (2021) [download preprint]

Abstract

Surface-driven flows are ubiquitous in nature, from subcellular cytoplasmic streaming to organ-scale ciliary arrays. Here, we model how confined geometries can be used to engineer complex hydrodynamic patterns driven by activity prescribed solely on the boundary. Specifically, we simulate light-controlled surface-driven active matter, probing the emergent properties of a suspension of active colloids that can bind and unbind pre-patterned surfaces of a closed microchamber, together creating an active carpet. The attached colloids generate large scale flows that in turn can advect detached particles towards the walls. Switching the particle velocities with light, we program the active suspension and demonstrate a rich design space of flow patterns characterised by topological defects. We derive the possible mode structures and use this theory to optimise different microfluidic functions including hydrodynamic compartmentalisation and chaotic mixing. Our results pave the way towards designing and controlling surface-driven active fluids.

Peer-reviewed journal articles

Publication 16

Micro-robots swimming upstream

16. Tuning upstream swimming of micro-robots by shape and cargo size

Daddi-Moussa-Ider* A, Lisicki* M and Mathijssen* AJTM
* Equal contributions

Physical Review Applied 14: 024071 (2020) [10.1103/PhysRevApplied.14.024071] [download PDF]

Abstract

The navigation of micro-robots in complex flow environments is controlled by rheotaxis, the reorientation with respect to flow gradients. Here we demonstrate how payloads can be exploited to enhance the motion against flows. Using fully resolved hydrodynamic simulations, the mechanisms are described that allow micro-robots of different shapes to reorient upstream. We find that cargo pullers are the fastest at most flow strengths, but pushers feature a non-trivial optimum as a function of the counter flow strength. Moreover, the rheotactic performance can be maximised by tuning the micro-robot shape or cargo size. These results may be used to control micro-swimmer navigation, but they also apply to rheotaxis in microbial ecology and the prevention of bacterial contamination dynamics.

Fundamental solution of flow in a droplet

15. Towards an analytical description of active microswimmers in clean and in surfactant-covered drops

Sprenger AR, Shaik VA, Ardekani AM, Lisicki M, Mathijssen AJTM, Guzmán-Lastra F, Löwen H, Menzel AM, Daddi-Moussa-Ider A

European Physics Journal E 43: 58 (2020) [10.1140/epje/i2020-11980-9] [download PDF]

Abstract

Geometric confinements are frequently encountered in the biological world and strongly affect the stability, topology, and transport properties of active suspensions in viscous flow. Based on a far-field analytical model, the low-Reynolds-number locomotion of a self-propelled microswimmer moving inside a clean viscous drop or a drop covered with a homogeneously distributed surfactant, is theoretically examined. The interfacial viscous stresses induced by the surfactant are described by the well-established Boussinesq-Scriven constitutive rheological model. Moreover, the active agent is represented by a force dipole and the resulting fluid-mediated hydrodynamic couplings between the swimmer and the confining drop are investigated. We find that the presence of the surfactant significantly alters the dynamics of the encapsulated swimmer by enhancing its reorientation. Exact solutions for the velocity images for the Stokeslet and dipolar flow singularities inside the drop are introduced and expressed in terms of infinite series of harmonic components. Our results offer useful insights into guiding principles for the control of confined active matter systems and support the objective of utilizing synthetic microswimmers to drive drops for targeted drug delivery applications.

Cilia in the respiratory system

14. Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays

Ramirez-San Juan GR, Mathijssen AJTM, He M, Jan L, Marshall WF, Prakash M

Nature Physics (2020) [10.1038/s41567-020-0923-8] [download PDF]

Media coverage (selection):

  • Nature News & Views, Pietro Cicuta, “Helpful disorder in the lungs”, published online & in print (8 June 2020)
  • Atlas of Science, “Disordered highways clear mucus from the lungs” (22 June 2020)
  • The Company of Biologists preLights, Mariana De Niz, “Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays” (9 June 2019)
Abstract

Mucus clearance constitutes the primary defence of the respiratory system against viruses, bacteria and environmental insults. This transport across the entire airway emerges from the integrated activity of thousands of multiciliated cells, each containing hundreds of cilia, which together must coordinate their spatial arrangement, alignment and motility. The mechanisms of fluid transport have been studied extensively at the level of an individual cilium, collectively moving metachronal waves and, more generally, the hydrodynamics of active matter. However, the connection between local cilia architecture and the topology of the flows they generate remains largely unexplored. Here, we image the mouse airway from subcellular (nm) to organ (mm) scales, characterizing quantitatively its ciliary arrangement and the generated flows. Locally, we measure heterogeneity in both cilia organization and flow structure, but, across the trachea, fluid transport is coherent. To examine this result, a hydrodynamic model was developed for a systematic exploration of different tissue architectures. Surprisingly, we find that disorder enhances particle clearance, whether it originates from fluctuations, heterogeneity in multiciliated cell arrangement or ciliary misalignment. This resembles elements of ‘stochastic resonance’, in the sense that noise can improve the function of the system. Taken together, our results shed light on how the microstructure of an active carpet determines its emergent dynamics. Furthermore, this work is also directly applicable to human airway pathologies, which are the third leading cause of deaths worldwide.

Hydrodynamic communication between cells 

13. Collective intercellular communication through ultra-fast hydrodynamic trigger waves

Mathijssen AJTM, Culver J, Bhamla MS, Prakash M

Nature 571: 560 (2019) [10.1038/s41586-019-1387-9] [download PDF]

Media coverage (selection):

  • Nature News & Views, Pavel Tomancak, “Cell communication in the blink of an eye”, published online & in print (10 July 2019)
  • Physics Today, Rachel Berkowitz, “Ultrafast signaling among aquatic single-celled organisms”, published online & in print (2 Aug 2019)
  • Stanford News, Taylor Kubota, “Ultra-fast communication allows aquatic cells to release toxins in unison” Taken over by various news websites, including: Sign of the Times, Phys.org, EurekAlert!, Science Daily, Long Room, Science and Life Russia, Futurity, Noticias de la Ciencia y la Technologia. (10 July 2019)
  • Lab Roots, Carmen Leitch, “A New Type of Cellular Communication is Discovered” (2 Aug 2019)
  • HFSP News, “Individual cells cooperate in colonies by communicating via ultra-fast flows” (Aug 2019)
  • APS DFD Gallery of Fluid Motion, “Collective hydrodynamic communication through ultra-fast cellular contractions” (18 Nov 2018)
Abstract

The biophysical relationships between sensors and actuators have been fundamental to the development of complex life forms. Swimming organisms generate abundant flows that persist in aquatic environments and responding promptly to external stimuli is key to survival. Here we present the discovery of ‘hydrodynamic trigger waves’ in cellular communities of the protist Spirostomum ambiguum that propagate—in a manner similar to a chain reaction—hundreds of times faster than their swimming speed. By coiling its cytoskeleton, Spirostomum can contract its long body by 60% within milliseconds, experiencing accelerations that can reach forces of 14g. We show that a single cellular contraction (the transmitter) generates long-ranged vortex flows at intermediate Reynolds numbers that can, in turn, trigger neighbouring cells (the receivers). To measure the sensitivity to hydrodynamic signals in these receiver cells, we present a high-throughput suction–flow device for probing mechanosensitive ion channels by back-calculating the microscopic forces on the cell membrane. We analyse and quantitatively model the ultra-fast hydrodynamic trigger waves in a universal framework of antenna and percolation theory, and reveal a phase transition that requires a critical colony density to sustain collective communication. Our results suggest that this signalling could help to organize cohabiting communities over large distances and influence long-term behaviour through gene expression (comparable to quorum sensing). In more immediate terms, because contractions release toxins, synchronized discharges could facilitate the repulsion of large predators or immobilize large prey. We postulate that numerous aquatic organisms other than protists could coordinate their behaviour using variations of hydrodynamic trigger waves.

Bacteria swimming diagonal against the flow

12. Oscillatory surface rheotaxis of swimming E. coli bacteria

Mathijssen AJTM, Figueroa-Morales N, Junot G, Lindner A, Clement E, Zöttl A

Nature Communications 10: 3434 (2019) [10.1038/s41467-019-11360-0] [download PDF]

Media coverage (selection):

Abstract

Bacterial contamination of biological channels, catheters or water resources is a major threat to public health, which can be amplified by the ability of bacteria to swim upstream. The mechanisms of this ‘rheotaxis’, the reorientation with respect to flow gradients, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow using 3D Lagrangian tracking and fluorescent flagellar labelling. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A theoretical analysis explains these rheotaxis regimes and predicts the corresponding critical shear rates. Our results shed light on bacterial transport and reveal strategies for contamination prevention, rheotactic cell sorting, and microswimmer navigation in complex flow environments.

An active particle pushing on a membrane

11. Membrane penetration and trapping of an active particle

Daddi-Moussa-Ider A, Lisicki M, Mathijssen AJTM, Hoell C, Goh S. Blawzdziewicz J, Menzel A, Löwen H

Journal of Chemical Physics 150: 064906 (2019) [10.1063/1.5080807] [download PDF]

Abstract

The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the particles can pass through cell membranes via passive endocytosis or by active penetration to reach a target cellular compartment or organelle. In this manuscript, we develop a simple model to describe the interaction of a self-driven spherical particle (moving through an effective constant active force) with a minimal membrane system, allowing for both penetration and trapping. We numerically calculate the state diagram of this system, the membrane shape, and its dynamics. In this context, we show that the active particle may either get trapped near the membrane or penetrate through it, where the membrane can either be permanently destroyed or recover its initial shape by self-healing. Additionally, we systematically derive a continuum description allowing us to accurately predict most of our results analytically. This analytical theory helps in identifying the generic aspects of our model, suggesting that most of its ingredients should apply to a broad range of membranes, from simple model systems composed of magnetic microparticles to lipid bilayers. Our results might be useful to predict the mechanical properties of synthetic minimal membranes.

PRL Cover

A bacterial colony attracting nutrients

10. Nutrient transport by microbial active carpets

Mathijssen AJTM, Guzman-Lastra F, Kaiser A, Löwen H

Physical Review Letters 121: 248101 (2018) [10.1103/PhysRevLett.121.248101] [download PDF]

Media coverage (selection):

  • Scientific Inquirer, interview, Marc Landas, “Conversations with Arnold Mathijssen: Strong vortex formation and biofilm nutrient supplies” (4 Mar 2019)
  • Stanford News, Taylor Kubota, “Stanford researcher deciphers flows that help bacteria feed and organize biofilms”. Taken over by Phys.org, EurekAlert!, Innovations Report, Long Room, LABO online, LaborPraxis, Futurity, Laboratory Equipment, BioScience Technology, Informationsdienst Wissenschaft  (12 Dec 2018)
  • Stanford Medicine Scope Blog, Taylor Kubota, “Biofilms feed with swirling flows” (17 Dec 2018)
  • HFSP News, “Microbial carpets generate vortex flows to attract nutrients” (Feb 2019)
  • El Mercurio (National newspaper in Chile), Janina Marcano F. “Las bacterias nadan juntas para alimentarse y ser más fuertes”, published online & in print (9 Jan 2019)
  • Las Últimas Noticias (National newspaper in Chile), D. Aguayo & F. Nuñez, “Físico de Stanford explica cómo functiona este microscopio que se puede armar en casa”, published online & in print (18 Dec 2018)
  • Physical Review Letters, on the cover
Abstract

We demonstrate that active carpets of bacteria or self-propelled colloids generate coherent flows towards the substrate, and propose that these currents provide efficient pathways to replenish nutrients that feed back into activity. A full theory is developed in terms of gradients in the active matter density and velocity, and applied to bacterial turbulence, topological defects and clustering. Currents with complex spatiotemporal patterns are obtained, which are tunable through confinement. Our findings show that diversity in carpet architecture is essential to maintain biofunctionality.

A model micro-robot in a channel

9. State diagram of a three-sphere microswimmer in a channel

Daddi-Moussa-Ider A, Lisicki M, Mathijssen AJTM, Hoell C, Goh S. Blawzdziewicz J, Menzel A, Löwen H

Journal of Physics: Condensed Matter 30: 254004 (2018) [10.1088/1361-648X/aac470] [download PDF]

Abstract

Geometric confinements are frequently encountered in soft matter systems and in particular significantly alter the dynamics of swimming microorganisms in viscous media. Surface-related effects on the motility of microswimmers can lead to important consequences in a large number of biological systems, such as biofilm formation, bacterial adhesion and microbial activity. On the basis of low-Reynolds-number hydrodynamics, we explore the state diagram of a three-sphere microswimmer under channel confinement in a slit geometry and fully characterize the swimming behavior and trajectories for neutral swimmers, puller- and pusher-type swimmers. While pushers always end up trapped at the channel walls, neutral swimmers and pullers may further perform a gliding motion and maintain a stable navigation along the channel. We find that the resulting dynamical system exhibits a supercritical pitchfork bifurcation in which swimming in the mid-plane becomes unstable beyond a transition channel height while two new stable limit cycles or fixed points that are symmetrically disposed with respect to the channel mid-height emerge. Additionally, we show that an accurate description of the averaged swimming velocity and rotation rate in a channel can be captured analytically using the method of hydrodynamic images, provided that the swimmer size is much smaller than the channel height.

Microplastics interacting with a swimming cell

8. Universal entrainment mechanism governs contact times with motile cells

Mathijssen* AJTM, Jeanneret* R, Polin M
* Equal contibutions

Physical Review Fluids 3: 033103 (2018) [10.1103/PhysRevFluids.3.033103] [download PDF]

Abstract

Contact between particles and motile cells underpins a wide variety of biological processes, from nutrient capture and ligand binding to grazing, viral infection, and cell-cell communication. The window of opportunity for these interactions depends on the basic mechanism determining contact time, which is currently unknown. By combining experiments on three different species—Chlamydomonas reinhardtii, Tetraselmis subcordiforms, and Oxyrrhis marina—with simulations and analytical modeling, we show that the fundamental physical process regulating proximity to a swimming microorganism is hydrodynamic particle entrainment. The resulting distribution of contact times is derived within the framework of Taylor dispersion as a competition between advection by the cell surface and microparticle diffusion, and predicts the existence of an optimal tracer size that is also observed experimentally. Spatial organization of flagella, swimming speed, and swimmer and tracer size influence entrainment features and provide tradeoffs that may be tuned to optimize the estimated probabilities for microbial interactions like predation and infection.

Flows generated by a bacterium in a film

7. Hydrodynamics of micro-swimmers in films

Mathijssen AJTM, Doostmohammadi A, Yeomans JM, Shendruk TN

Journal of Fluid Mechanics 806: 35-70 (2016) [10.1017/jfm.2016.479] [download PDF]

Abstract

One of the principal mechanisms by which surfaces and interfaces affect microbial life is by perturbing the hydrodynamic flows generated by swimming. By summing a recursive series of image systems, we derive a numerically tractable approximation to the three-dimensional flow fields of a stokeslet (point force) within a viscous film between a parallel no-slip surface and a no-shear interface and, from this Green’s function, we compute the flows produced by a force- and torque-free micro-swimmer. We also extend the exact solution of Liron & Mochon (J. Engng Maths, vol. 10 (4), 1976, pp. 287–303) to the film geometry, which demonstrates that the image series gives a satisfactory approximation to the swimmer flow fields if the film is sufficiently thick compared to the swimmer size, and we derive the swimmer flows in the thin-film limit. Concentrating on the thick-film case, we find that the dipole moment induces a bias towards swimmer accumulation at the no-slip wall rather than the water–air interface, but that higher-order multipole moments can oppose this. Based on the analytic predictions, we propose an experimental method to find the multipole coefficient that induces circular swimming trajectories, allowing one to analytically determine the swimmer’s three-dimensional position under a microscope.

Focussing microbes toward the centerline

6. Understanding the onset of oscillatory swimming in microchannels

Graaf de J, Mathijssen AJTM, Fabritius M, Menke H, Holm C, Shendruk TN

Soft Matter 12: 4704-4708 (2016) [10.1039/C6SM00939E] [download PDF]

Abstract

Self-propelled colloids (swimmers) in confining geometries follow trajectories determined by hydrodynamic interactions with the bounding surfaces. However, typically these interactions are ignored or truncated to the lowest order. We demonstrate that higher-order hydrodynamic moments cause rod-like swimmers to follow oscillatory trajectories in quiescent fluid between two parallel plates, using a combination of lattice-Boltzmann simulations and far-field calculations. This behavior occurs even far from the confining walls and does not require lubrication results. We show that a swimmer’s hydrodynamic quadrupole moment is crucial to the onset of the oscillatory trajectories. This insight allows us to develop a simple model for the dynamics near the channel center based on these higher hydrodynamic moments, and suggests opportunities for trajectory-based experimental characterization of swimmers’ hydrodynamic properties.

Flows generated by anisotropic active matter

5. Lattice-Boltzmann hydrodynamics of anisotropic active matter

Graaf de J, Menke H, Mathijssen AJTM, Fabritius M, Holm C, Shendruk TN

Journal of Chemical Physics 144: 134106 (2016) [10.1063/1.4944962] [download PDF]

Abstract

A plethora of active matter models exist that describe the behavior of self-propelled particles (or swimmers), both with and without hydrodynamics. However, there are few studies that consider shape-anisotropic swimmers and include hydrodynamic interactions. Here, we introduce a simple method to simulate self-propelled colloids interacting hydrodynamically in a viscous medium using the lattice-Boltzmann technique. Our model is based on raspberry-type viscous coupling and a force/counter-force formalism, which ensures that the system is force free. We consider several anisotropic shapes and characterize their hydrodynamic multipolar flow field. We demonstrate that shape-anisotropy can lead to the presence of a strong quadrupole and octupole moments, in addition to the principle dipole moment. The ability to simulate and characterize these higher-order moments will prove crucial for understanding the behavior of model swimmers in confining geometries.

Microbes swimming against the flow. In a shear-thinning fluid (top) they move slower than in a shear-thickening fluid (bottom).

4. Upstream Swimming in Microbiological Flows

Mathijssen AJTM, Shendruk TN, Yeomans JM, Doostmohammadi A

Physical Review Letters 116: 028104 (2016) [10.1103/PhysRevLett.116.028104] [download PDF]

Abstract

Interactions between microorganisms and their complex flowing environments are essential in many biological systems. We develop a model for microswimmer dynamics in non-Newtonian Poiseuille flows. We predict that swimmers in shear-thickening (-thinning) fluids migrate upstream more (less) quickly than in Newtonian fluids and demonstrate that viscoelastic normal stress differences reorient swimmers causing them to migrate upstream at the centerline, in contrast to well-known boundary accumulation in quiescent Newtonian fluids. Based on these observations, we suggest a sorting mechanism to select microbes by swimming speed.

Bacteria swimming a flowing film

3. Hotspots of boundary accumulation: dynamics and statistics of microswimmers
in flowing films

Mathijssen AJTM, Doostmohammadi A, Yeomans JM, Shendruk TN

Journal of the Royal Society Interface 13: 115 (2016) [10.1098/rsif.2015.0936] [download PDF]

Media coverage (selection):

Abstract

Biological flows over surfaces and interfaces can result in accumulation hotspots or depleted voids of microorganisms in natural environments. Apprehending the mechanisms that lead to such distributions is essential for understanding biofilm initiation. Using a systematic framework, we resolve the dynamics and statistics of swimming microbes within flowing films, considering the impact of confinement through steric and hydrodynamic interactions, flow and motility, along with Brownian and run–tumble fluctuations. Micro-swimmers can be peeled off the solid wall above a critical flow strength. However, the interplay of flow and fluctuations causes organisms to migrate back towards the wall above a secondary critical value. Hence, faster flows may not always be the most efficacious strategy to discourage biofilm initiation. Moreover, we find run–tumble dynamics commonly used by flagellated microbes to be an intrinsically more successful strategy to escape from boundaries than equivalent levels of enhanced Brownian noise in ciliated organisms.

A cell entraining micro-particles near a surface

2. Tracer trajectories and displacement due to a micro-swimmer near a surface

Mathijssen AJTM, Pushkin DO, Yeomans JM

Journal of Fluid Mechanics 733: 498-519 (2015) [10.1017/jfm.2015.269] [download PDF]

Abstract

We study tracer particle transport due to flows created by a self-propelled micro-swimmer, such as a swimming bacterium, alga or a microscopic artificial swimmer. Recent theoretical work has shown that as a swimmer moves in the fluid bulk along an infinite straight path, tracer particles far from its path perform closed loops, whereas those close to the swimmer are entrained by its motion. However, in biologically and technologically important cases tracer transport is significantly altered for swimmers that move in a run-and-tumble fashion with a finite persistence length, and/or in the presence of a free surface or a solid boundary. Here we present a systematic analytical and numerical study exploring the resultant regimes and their crossovers. Our focus is on describing qualitative features of the tracer particle transport and developing quantitative tools for its analysis. Our work is a step towards understanding the ecological effects of flows created by swimming organisms, such as enhanced fluid mixing and biofilm formation.

Distribution in χ2 values versus x for fits to a valence-like quark distribution

1. Extended parameterisations for MSTW PDFs and their effect on lepton charge asymmetry from W decays

Martin* AD, Mathijssen* AJTM, Stirling* WJ, Thorne* RS, Watt* BJA, and Watt* G
* All authors contributed equally. Alphabetical ordering.

European Physics Journal C 73:2318 (2013) [10.1140/epjc/s10052-013-2318-9] [download PDF]

Abstract

We investigate the effect of extending the standard MSTW parameterisation of input parton distribution functions (PDFs) using Chebyshev polynomials, rather than the usual expressions which involve a factor of the form (1+ϵx 0.5+γx). We find evidence that four powers in the polynomial are generally sufficient for high precision. Applying this to valence and sea quarks, the gluon already being sufficiently flexible and needing only two powers, we find an improvement in the global fit, but a significant change only in the small-x valence up-quark PDF, u V . We investigate the effect of also extending, and making more flexible, the ‘nuclear’ correction to deuteron structure functions. We show that the extended ‘Chebyshev’ parameterisation results in an improved stability in the deuteron corrections that are required for the best fit to the ‘global’ data. The resulting PDFs have a significantly, but not dramatically, altered valence down-quark distribution, d V . It is shown that, for the extended set of MSTW PDFs, their uncertainties can be obtained using 23, rather than the usual 20, orthogonal ‘uncertainty’ eigenvectors. This is true both without and with extended deuteron corrections. Since the dominant effect is on the valence quarks, we present a detailed study of the dependence of the valence–sea separation on the predictions for the decay lepton charge asymmetry which results from W ± production at the LHC, illustrating the PDFs and the x range probed for different experimental scenarios. We show that the modified MSTW PDFs make significantly improved predictions for these data at the LHC, particularly for high values of the p T cut of the decay lepton. However, this is a special case, since the asymmetry is extremely sensitive to valence–sea details, and in particular to the combination u V −d V of valence PDFs at low lepton rapidities. We show that the predictions for a wide variety of total cross sections are very similar to those obtained using the MSTW2008 PDFs, with changes being much smaller than the PDF uncertainties.

Patents

A microfluidic device for sorting microplastics

1. Microfluidic device for hydrodynamic sorting and rheometry measurements of particles

Mossige* EJ, Mathijssen* AJTM
* Equal contributions

US patent pending, no. 62/816574 (2019)

Abstract
This invention relates to particle sorting and particle rheometry in fluidic devices.

Particles, cells and other biomaterials frequently adhere to obstacles and filter surfaces used for sorting and filtration. As a result, they clog up filters which have to be changed regularly. This clogging problem strongly limits their performance and reliability. Fluidic devices used for particle rheometry — the study of stress-strain relations in particles — are also affected by this clogging problem. Accordingly, it would be an advance in the art to provide intrinsically clog-free particle sorting and rheometry.

Theses

Hydrodynamics of a microbe in a channel

PhD Thesis: Dynamics and statistics of micro-swimmers in complex fluids and environments

Supervised by Prof. Julia M Yeomans FRS

University of Oxford, ISNI 0000-0004-6421-4868 (2016)
[download from the British Library]

Abstract
Both biological micro-organisms and synthetic micro-robots propel through viscous liquids to achieve their goal, be it to invade new territories or to deliver drugs to infected regions. Considerable attention is devoted to learning how to prevent or encourage these processes, and understanding the interactions between micro-swimmers and their complex environments is an essential part of this. In vivo conditions provide a challenge to model, although novel experimental, computational and theoretical techniques have provided clear insights into the continuous interplay between the effects of strong confinement, hydrodynamic interactions, and local activity that drives living systems out of equilibrium.

To analyse the underlying mechanisms of micro-swimmer processes, we develop a hydrodynamic framework based on the fundamental solutions of the Stokes equations to compute swimmer-generated flow fields. These flows affect the motion of swimmers via reflections in surfaces, mix and enhance the uptake of nutrients, and enable cells to sense one another’s presence.

Hence, we study the accumulation of microbes on surfaces, which could be relevant for the initial stages of biofilm formation, and compute the strength required for externally imposed flows to detach them. Moreover, we evaluate the ability to swim upstream and uncover that viscoelasticity can provide a natural sorting mechanism for sperm cells. Other ecological effects are considered, including the transport of nutrients by micro-flows, the interaction with water-air interfaces, and the impact of thermal noise and biological fluctuations.

To verify our results, we compare our theory to extensive simulations using a “Raspberry” swimmer model in combination with the Lattice-Boltzmann fluid solver algorithm.This allows us to determine previously unknown model parameters and hence make suggestions to improve micro-organism treatment and micro-robot design.

Large Hadron Collider

Master Thesis: Determining the quark and gluon composition of the proton

Supervised by Prof. Robert S Thorne

University of College London, MSTW collaboration (2012)

Abstract

We investigate the effect of extending the standard MSTW parameterisation of input parton distribution functions (PDFs) using Chebyshev polynomials, rather than the usual expressions which involve a factor of the form (1+ϵx 0.5+γx). We find evidence that four powers in the polynomial are generally sufficient for high precision. Applying this to valence and sea quarks, the gluon already being sufficiently flexible and needing only two powers, we find an improvement in the global fit, but a significant change only in the small-x valence up-quark PDF, u V . We investigate the effect of also extending, and making more flexible, the ‘nuclear’ correction to deuteron structure functions. We show that the extended ‘Chebyshev’ parameterisation results in an improved stability in the deuteron corrections that are required for the best fit to the ‘global’ data. The resulting PDFs have a significantly, but not dramatically, altered valence down-quark distribution, d V . It is shown that, for the extended set of MSTW PDFs, their uncertainties can be obtained using 23, rather than the usual 20, orthogonal ‘uncertainty’ eigenvectors. This is true both without and with extended deuteron corrections. Since the dominant effect is on the valence quarks, we present a detailed study of the dependence of the valence–sea separation on the predictions for the decay lepton charge asymmetry which results from W ± production at the LHC, illustrating the PDFs and the x range probed for different experimental scenarios. We show that the modified MSTW PDFs make significantly improved predictions for these data at the LHC, particularly for high values of the p T cut of the decay lepton. However, this is a special case, since the asymmetry is extremely sensitive to valence–sea details, and in particular to the combination u V −d V of valence PDFs at low lepton rapidities. We show that the predictions for a wide variety of total cross sections are very similar to those obtained using the MSTW2008 PDFs, with changes being much smaller than the PDF uncertainties.

Fluorescence image of a neuron

BSc Thesis: Design of a single-molecule fluorescence microscope system

Supervised by Prof. Angus Bain

University of College London (2011)

Abstract

The aim of this project is to develop a low-cost detection system to probe single molecules using fluorescence detection techniques. The final result is a carefully selected combination of components that all live up to high quality yet relatively low cost standards. Calculations of the Signal-to-Noise ratio confirm that the final compilation is more than sufficient to achieve single molecule detection and perform time-dependent fluorescence studies.